Scripts.DatabankLib.settings.molecules module

module:: settings/molecules.py
description:: Module file with definition of different global-level dictionaries.

There is a dictionary of lipids, ions, etc. If you add a lipid which is not yet in the databank, you have to add it here!

class Scripts.DatabankLib.settings.molecules.Molecule(name: str)[source]

Bases: ABC

Abstract base class representing a molecule and its related operations.

This class is designed to provide an interface for interacting with molecule-related files, which are stored in a molecule-related folder. It serves as a base for concrete implementations that need to define specific operations for handling molecule data.

register_mapping(fname: str) → None[source]

Register mapping dictionary for the Molecule object

Parameters:: fname – mapping filename (without path)
Returns:

property mapping_dict: dict

property name: str

Molecule name.

Type:: return

class Scripts.DatabankLib.settings.molecules.Lipid(name: str)[source]

Bases: Molecule

Lipid class inherited from Molecule base. Contains all the molecules which belongs to the bilayer.

class Scripts.DatabankLib.settings.molecules.NonLipid(name: str)[source]

Bases: Molecule

Class for non-bilayer molecules: solvent, ions, etc.

class Scripts.DatabankLib.settings.molecules.MoleculeSet(*args)[source]

Bases: MutableSet[Molecule], ABC

MoleculeSet is a Set (repeating normal set functionality) but with some additional molecule-specific things.

add(item: Molecule)[source]

Add a lipid to the set.

Parameters:: item – Can add either Molecule or str (then Molecule constructor will be called)

discard(item)[source]: Remove a lipid from the set without raising an error if it does not exist.

property names: set[str]

class Scripts.DatabankLib.settings.molecules.LipidSet(*args)[source]

Bases: MoleculeSet

MoleculeSet specialization for Lipid.

static load_from_data()[source]

Loads lipid data from the designated directory and returns a set of lipids.

Return type:: LipidSet
Returns:: An instance of loaded LipidSet.

class Scripts.DatabankLib.settings.molecules.NonLipidSet(*args)[source]

Bases: MoleculeSet

MoleculeSet specialization for NonLipid.

static load_from_data()[source]

Loads Nonlipid data from the designated directory and returns a set of lipids.

Return type:: NonLipidSet
Returns:: An instance of loaded NonLipidSet.

Scripts.DatabankLib.settings.molecules.lipids_set: LipidSet = LipidSet[{'TOCL', 'CHOL', 'POPC', 'POPE', 'DPPC'}]: Dictionary of possible lipids

Scripts.DatabankLib.settings.molecules.lipids_dict = LipidSet[{'TOCL', 'CHOL', 'POPC', 'POPE', 'DPPC'}]

Use lipids_set instead.

Type:: @deprecated

Scripts.DatabankLib.settings.molecules.molecules_set: NonLipidSet = NonLipidSet[{'SOL', 'CLA', 'SOD'}]: Dictionary of other than lipid molecules.

Scripts.DatabankLib.settings.molecules.molecules_dict = NonLipidSet[{'SOL', 'CLA', 'SOD'}]

Use molecules_set instead

Type:: @deprecated

Scripts.DatabankLib.settings.molecules.molecule_ff_set = {'FFCHOL', 'FFCLA', 'FFDPPC', 'FFPOPC', 'FFPOPE', 'FFSOD', 'FFSOL', 'FFTOCL'}: Dictionary containing possible force-field labels for molecules given by the contributor (used for README/info fields validation)